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<h1>Semantics of Biodiversity Workshop May 16 - 18, 2012
<br />University of Kansas Biodiversity Institute  -- Lawrence, Kansas</h1>
<p><strong><a href="../images/GroupPhoto800.jpg"><img src="../images/GroupPhoto400.jpg" alt="Group Photo" width="400" height="277" hspace="10" vspace="10" align="left" /></a></strong></p>
<strong>Sponsored by <a href="http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.26218">RCN4GSC</a> (NSF), <a href="http://www.morphbank.net/">Morphbank</a> (NSF), <a href="http://biodiversity.ku.edu/">Kansas University&rsquo;s Biodiversity Institut</a>e, and <a href="http://biscicol.blogspot.com/">BiSciCol</a> (NSF), in collaboration with the <a href="http://www.bioontology.org/">National Center for Biomedical Ontology</a>, with content-hosting by <a href="http://biocodecommons.org/">Biocode Commons</a></strong>.
<p>
  <b>The Speaker: </b>Barry Smith is a prominent contributor to ontology research in biomedical and other domains. He is one of the principal scientists of the NIH National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, a PI on the Protein Ontology and Infectious Disease Ontology projects, and one of the founders of the <a href="http://obofoundry.org/">Open Biomedical Ontologies (OBO) </a>Foundry initiative.<br />
<p>
<b>Topics: </b>The Semantics of Biodiversity Workshop will explore terms used to describe biological collection objects and their derivatives using the Darwin Core standard as a starting point.  The goal is to enable linking data across domains and to produce a deeper understanding of our planet&rsquo;s biodiversity. For example, by linking information about the ecosystem (both gross and micro-habitat) and the geospatial environment to tissue samples and derived sequences, we can better understand population dynamics, ecosystem gene expression, and the significance of biodiversity in different environments.
Before the workshop, users provided a list of <a href="https://docs.google.com/document/d/1hYBba6zuJjHhvQ7MU8ZPa_G8dmOAIOYxgfaZP7dKCiE/edit">challenging issues and terms</a>.
<p>The <a href="https://docs.google.com/document/d/1Z-RytvBlinIcSD3ctK1kiWUs2rr4TOxijT2TQb9L0Vk/edit">Full Agenda</a> is available online.
<p><br>
  <b>Day 1: Wednesday, May 16, 2012</b><br>
<p>Video: <a href="http://www.youtube.com/watch?v=ZrHYi7mgF9g">AM 1</a>, Barry Smith
<ul>
  <li>Ontologies as method of viewing data neutrally</li>
  <li>Analogies to biomedical domain</li>
  <li>Other ontologies we can learn from<br>
  </li>
</ul>
<p><a href="http://www.youtube.com/watch?v=Fot1dOPLv_c">AM 2</a>, Barry Smith
<ul>
  <li>Basic Formal Ontology</li>
  <li>Continuants/ Occurrents</li>
  <li>Types and relations<br>
  </li>
</ul>
<p><a href="http://www.youtube.com/watch?v=rWy3C0WmpZM">PM 1</a>, Barry Smith
<ul>
  <li>How to build an ontology with BFO</li>
  <li>Example with measurements in biomedical domain<br>
  </li>
</ul>
<p><a href="http://www.youtube.com/watch?v=kaG92j0WqmI">PM 2</a>, Barry Smith
<ul>
  <li>Tracking referents</li>
  <li>Instance Unique Identifiers (IUI's)<br>
  </li>
</ul>
<p><a href="http://www.youtube.com/watch?v=fHP0Dlk5wuo">PM 3</a>, Barry Smith
<ul>
  <li>Tracking changes in our understanding of reality</li>
  <li>Reality vs. beliefs</li>
  <li>Sources of error</li>
  <li>Reconciling different views of reality</li>
  <li>The Information Artifact Ontology</li>
</ul>
<p>
  <b>Day 2: Thursday, May 17, 2012</b><br>
<p><a href="http://www.youtube.com/watch?v=FA8eJOeV-Z4">Video: Darwin Core Summary</a>, John Wieczorek, UC Berkeley<br>
<p><a href="http://www.youtube.com/watch?v=yiICcMbE2Ik">Germplasm Extension</a>, Dag Endresen, Global Biodiversity Information Facility<br>
<p><a href="http://www.youtube.com/watch?v=cAbvBFIY35o">Darwin-SW</a>, Joel Sachs, TDWG RDF Interest Group
<p><a href="http://www.youtube.com/watch?v=4mVZz7ZNavU">The Environment Ontology</a>, Norman Morrison, University of Manchester, UK
<p><a href="http://www.youtube.com/watch?v=Of6bj28MQhY">Darwin Core and Basic Formal Ontology (putting it all together + wrapup)</a> , Barry Smith
<ul>
  <li>Building Darwin Core top-down in BFO</li>
  <li>Organisms, photographs, media</li>
  <li>How to re-use ontologies</li>
  <li>Principles of singular nouns, secondary use, understandability</li>
  <li>Writing good definitions (DwC Examples)</li>
  <li>Management Strategies</li>
  <li>Ontologies of relevance for reuse (BFO, EnvO, IDO, OBI, Plant Ontology , Uberon, IAO)</li>
  <li>Educational Resources (OBI, Protege, BFO)</li>
</ul>
<p><a href="http://youtu.be/rumlDesLtV0">Participant discussion and breakout group organization for Friday</a>, Bob Robbins, University of California, San Diego

<p><b>Day 3: Breakout Groups, Friday May 18, 2012</b><p><a href="https://docs.google.com/document/d/1tF2rVxATUo8hxOifuucQ4LJAIK4Hz88fPkpw5wKyTKo/edit">Individual Breakouts document</a>
(with links to DwC/BFO, Governance, relations, and Testbed groups)
<p><strong>Post-Workshop References</strong>
<p><a href="http://bioportal.bioontology.org/ontologies/47531">DwC Ontology in BioPortal</a> - The beginnings of this Ontology was sketched during the last day of the workshop and subsequently added to BioPortal.<br />
<p><a href="http://rs.tdwg.org/dwc/terms/">Darwin Core Terms Reference</a> - An up to date list of darwin core terms.
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